General information for g10361.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as SWI/SNF complex subunit SMARCC2.
Parent gene
- The parent gene g10361 is located on chr_1: 9106070..9109573 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_1 | g10361 | g10361.t2 | TSS | g10361.t2 | 9105990 | 9105990 |
| chr_1 | g10361 | g10361.t2 | isoform | g10361.t2 | 9106070 | 9107181 |
| chr_1 | g10361 | g10361.t2 | exon | g10361.t2.exon1 | 9106070 | 9106183 |
| chr_1 | g10361 | g10361.t2 | cds | g10361.t2.CDS1 | 9106070 | 9106183 |
| chr_1 | g10361 | g10361.t2 | exon | g10361.t2.exon2 | 9106265 | 9106387 |
| chr_1 | g10361 | g10361.t2 | cds | g10361.t2.CDS2 | 9106265 | 9106387 |
| chr_1 | g10361 | g10361.t2 | exon | g10361.t2.exon3 | 9106447 | 9106560 |
| chr_1 | g10361 | g10361.t2 | cds | g10361.t2.CDS3 | 9106447 | 9106560 |
| chr_1 | g10361 | g10361.t2 | exon | g10361.t2.exon4 | 9106620 | 9107181 |
| chr_1 | g10361 | g10361.t2 | cds | g10361.t2.CDS4 | 9106620 | 9107180 |
| chr_1 | g10361 | g10361.t2 | TTS | g10361.t2 | 9107188 | 9107188 |
Sequences
>g10361.t2 Gene=g10361 Length=913
ATGAATTTAGGACCGAAAAAAGATGGAAGTCCAAATGTAGAGTTTTTTACATCACCTGAA
TCACTTCAGGGATTCGAGACTGTTCGATTATGGCTACAAAAACATCATAAAAAATATATT
CAGGCTGATCCACCAACAAAAGAGAGCCTTGCACAGCTCATTATTCAATTAATACAGTAT
CAAGAAACAAAACTTGGTAAAAATTCTCAAGATACATCGATGACAACAAGACTTCCGATG
AGATTTTTTCATGATTTCAAACCTGGTGGAGCACTTTGTGTCATTTTATCAACAATGTAT
CGCTTCAAGAGTGATCAACGTTGGAGAAAATTTGATTTCACTGTTAGCAAAACATCATCC
AAAAAAGATCCAAATCTTCAATTGCTTGTTGAAATTGAATCAAGTTTGATTGACGCTGAA
GTTTTTAGACTTCCAACAATTTACATTAGACCAGAAGTTGATCGACAACTTGCAGCAAGA
ATACGTGAAATTATTACAAATCATCAAGCTGAAATAACAGAAGATGAAGAAGAAGCGACA
CATATTGTGTATCCAGAAGTTGATCCTCTGCCTGAAGAATATGCGAGACCGCTATTTAAA
CGTGACAAATATGTCATGCTGCATTGGTATTATTTTCCAGAATCATACGATTCTTGGGTT
CCAAATAATTTCGATTTACCTGACAATGTTCCCGATTGTCCTGCATCACCTGCCGATCAT
TGGCGTGTTTCTGCTCAGTGGGTTCGTGATCTTGATCAATATAATGAATGGATGTCAGAA
GAAGATTATGAAGTTGATGAACAAGGACGTAAGAAAGTTCATAAATTAAGAATTTCTGTT
GAAGATCTTATGTCAGCTGATGGTGATAAGTCAAAGAAACAAATGGCATCAAAAGGTAAA
CGTAAGCGCTCAC
>g10361.t2 Gene=g10361 Length=304
MNLGPKKDGSPNVEFFTSPESLQGFETVRLWLQKHHKKYIQADPPTKESLAQLIIQLIQY
QETKLGKNSQDTSMTTRLPMRFFHDFKPGGALCVILSTMYRFKSDQRWRKFDFTVSKTSS
KKDPNLQLLVEIESSLIDAEVFRLPTIYIRPEVDRQLAARIREIITNHQAEITEDEEEAT
HIVYPEVDPLPEEYARPLFKRDKYVMLHWYYFPESYDSWVPNNFDLPDNVPDCPASPADH
WRVSAQWVRDLDQYNEWMSEEDYEVDEQGRKKVHKLRISVEDLMSADGDKSKKQMASKGK
RKRS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g10361.t2 | Coils | Coil | Coil | 158 | 178 | - |
| 3 | g10361.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 284 | 304 | - |
| 1 | g10361.t2 | Pfam | PF16496 | SWIRM-associated domain at the N-terminal | 5 | 304 | 5.5E-140 |
| 2 | g10361.t2 | SUPERFAMILY | SSF52113 | BRCT domain | 141 | 271 | 2.5E-12 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed